arXiv subjects

D. Gamermann

Publications and source records attributed to D. Gamermann.

At least 19 recordsLinked to original sources

arXiv2017

A comprehensive statistical study of metabolic and protein-protein interaction network properties

Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs representing metabolic and protein-protein interaction (PPI) networks. First, we investigate the quality of fits obtained for the nodes degree distributions to power-law functions. This analysis suggests that a power-law distribution poorly describes the data except for the far right tail in the case of PPI networks. Next we obtain descriptive statistics for the main graph parameters and try to identify the properties that deviate from the expected values had the networks been built by randomly linking nodes with the same degree distribution. This survey identifies the properties of biological networks which are not solely the result of their degree distribution, but emerge from yet unidentified mechanisms other than those that drive these distributions. The findings suggest that, while PPI networks have properties that differ from their expected values in their randomized versions with great statistical significance, the differences for metabolic networks have a smaller statistical significance, though it is possible to identify some drift.

q-bio.MN↗

arXiv2013

Charming Baryons

We study odd-parity baryonic resonances with one heavy and three light flavors, dynamically generated by meson-baryon interactions. Special attention is paid to Heavy Quark Spin Symmetry (HQSS), hence pseudoscalar and vector mesons and baryons with J^P = 1/2+ and 3/2+ are considered as constituent hadrons. For the hidden-charm sector (N-c-quarks = N-c-antiquarks = 1), the meson-baryon Lagrangian with Heavy Flavor Symmetry is constructed by a minimal extension of the SU(3) Weinberg-Tomozawa (WT) Lagrangian to fulfill HQSS, such that not new parameters are needed. This interaction can be presented in different formal ways: as a Field Lagrangian, as Hadron creation-annihilation operators, as SU(6)xHQSS group projectors and as multichannel matrices. The multichannel Bethe-Salpeter equation is solved for odd-parity light baryons, hidden-charm N and Delta and Beauty Baryons (Lambda-b). Results of calculations with this model are shown in comparison with other models and experimental values for baryonic resonances.

hep-ph↗

arXiv2012

PyNetMet: Python tools for efficient work with networks and metabolic models

Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an essential element in their research. Therefore there is a strong need of efficient and versatile computational tools for the research in this area. Results: In this manuscript we present PyNetMet, a Python library of tools to work with networks and metabolic models. These are open-source free tools for use in a Python platform, which adds considerably versatility to them when compared with their desktop software similars. On the other hand these tools allow one to work with different standards of metabolic models (OptGene and SBML) and the fact that they are programmed in Python opens the possibility of efficient integration with any other already existing Python tool. Conclusions: PyNetMet is, therefore, a collection of computational tools that will facilitate the research work with metabolic models and networks.

q-bio.MN↗

arXiv2012

Phylogenetic tree reconstruction from genome-scale metabolic models

A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this comparison in order to infer evolutionary distances between different organisms. Our methodology allows a quantification of the metabolic differences between different species from a broad range of families and even kingdoms. This quantification is then applied in order to reconstruct phylogenetic trees for sets of various organisms.

q-bio.MN↗

arXiv2012

Automation on the generation of genome scale metabolic models

Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory collect, analyze and validate the list of all metabolic reactions present in a specific organism. In order to write this list, one manually has to go through a huge amount of genomic, metabolomic and physiological information. Currently, there is no optimal algorithm that allows one to automatically go through all this information and generate the models taking into account probabilistic criteria of unicity and completeness that a biologist would consider. Results: This work presents the automation of a methodology for the reconstruction of genome scale metabolic models for any organism. The methodology that follows is the automatized version of the steps implemented manually for the reconstruction of the genome scale metabolic model of a photosynthetic organism, {\it Synechocystis sp. PCC6803}. The steps for the reconstruction are implemented in a computational platform (COPABI) that generates the models from the probabilistic algorithms that have been developed. Conclusions: For validation of the developed algorithm robustness, the metabolic models of several organisms generated by the platform have been studied together with published models that have been manually curated. Network properties of the models like connectivity and average shortest mean path of the different models have been compared and analyzed.

q-bio.MN↗

arXiv2011

A modular synthetic device to calibrate promoters

In this contribution, a design of a synthetic calibration genetic circuit to characterize the relative strength of different sensing promoters is proposed and its specifications and performance are analyzed via an effective mathematical model. Our calibrator device possesses certain novel and useful features like modularity (and thus the possibility of being used in many different biological contexts), simplicity, being based on a single cell, high sensitivity and fast response. To uncover the critical model parameters and the corresponding parameter domain at which the calibrator performance will be optimal, a sensitivity analysis of the model parameters was carried out over a given range of sensing protein concentrations (acting as input). Our analysis suggests that the half saturation constants for repression, sensing and difference in binding cooperativity (Hill coefficients) for repression are the key to the performance of the proposed device. They furthermore are determinant for the sensing speed of the device, showing that it is possible to produce detectable differences in the repression protein concentrations and in turn in the corresponding fluorescence in less than two hours. This analysis paves the way for the design, experimental construction and validation of a new family of functional genetic circuits for the purpose of calibrating promoters.

q-bio.MN↗

arXiv2011

Odd Parity Light Baryon Resonances

We use a consistent SU(6) extension of the meson-baryon chiral Lagrangian within a coupled channel unitary approach in order to calculate the T-matrix for meson-baryon scattering in s-wave. The building blocks of the scheme are the pion and nucleon octets, the rho nonet and the Delta decuplet. We identify poles in this unitary T-matrix and interpret them as resonances. We study here the non exotic sectors with strangeness S=0,-1,-2,-3 and spin J=1/2, 3/2 and 5/2. Many of the poles generated can be associated with known N, Delta, Sigma, Lambda and Xi resonances with negative parity. We show that most of the low-lying three and four star odd parity baryon resonances with spin 1/2 and 3/2 can be related to multiplets of the spin-flavor symmetry group SU(6). This study allows us to predict the spin-parity of the Xi(1620), Xi(1690), Xi(1950), Xi(2250), Omega(2250) and Omega(2380) resonances, which have not been determined experimentally yet.

hep-ph↗

arXiv2011

Selected topics on Hadrons in Nuclei

In this talk we report on selected topics on hadrons in nuclei. The first topic is the renormalization of the width of the $\Lambda(1520)$ in a nuclear medium. This is followed by a short update of the situation of the $\omega$ in the medium. The investigation of the properties of $\bar{K}$ in the nuclear medium from the study of the $(K_{flight},p)$ reaction is also addressed, as well as properties of X,Y,Z charmed and hidden charm resonances in a nuclear medium. Finally we address the novel issue of multimeson states.

nucl-th↗

arXiv2011

The X(3872) and other X,Y,Z Resonances as Hidden Charm Meson-Meson Molecules

We report on some ideas concerning the nature of the X(3872) resonance and the need for approximately equal charged and neutral components of $D \bar{D}^* +cc$. Then we discuss how some hidden charm states are obtained from the interaction between vector mesons with charm and can be associated to some of the charmonium-like X,Y,Z states. Finally we discuss how the nature of these states could be investigated through different types of radiative decay.

hep-ph↗

arXiv2010

Radiative decays of dynamically generated charmed baryons

In this work we study the radiative decay of dynamically generated $J^P=\oh^-$ charm baryons into the ground state $J^P=\oh^+$ baryons. Since different theoretical interpretations of these baryonic resonances, and in particular of the $\Lambda_c(2595)$, give different predictions, a precise experimental measurement of these decays would be an important step for understanding their nature.

hep-ph↗

arXiv2010

Exotic dynamically generated baryons with C$=-$1

We follow a model based on the SU(8) symmetry for the interaction of mesons with baryons. The model treats on an equal footing the pseudo-scalars and the vector mesons, as required by heavy quark symmetry. The T-matrix calculated within an unitary scheme in coupled channels has poles which are interpreted as baryonic resonances.

hep-ph↗

arXiv2010

Heavy meson production in hot dense matter

The properties of charmed mesons in dense matter are studied using a unitary coupled-channel approach in the nuclear medium which takes into account Pauli-blocking effects and meson self-energies in a self-consistent manner. We obtain the open-charm meson spectral functions in this dense nuclear environment, and discuss their implications on hidden charm and charm scalar resonances and on the formation of $D$-mesic nuclei at FAIR energies.

nucl-th↗

arXiv2010

Exotic dynamically generated baryons with negative charm quantum number

Following a model based on the $\rm{SU}(8)$ symmetry that treats heavy pseudo-scalars and heavy vector mesons on an equal footing, as required by heavy quark symmetry, we study the interaction of baryons and mesons in coupled channels within an unitary approach that generates dynamically poles in the scattering $T$-matrix. We concentrate in the exotic channels with negative charm quantum number for which there is the experimental claim of one state.

hep-ph↗

arXiv2010

Isospin breaking effects in the dynamical generation of the X(3872)

We have studied isospin breaking effects in the X(3872) resonance and found a natural explanation for the branching fraction of the X decaying to $J/\psi$ with two and three pions being close to unit. Within our framework the X(3872) is a dynamically generated resonance in coupled channels. We also study the relationship between the couplings of the resonance to the coupled channels with its wave function, which further helps us to understand the isospin structure of the resonance.

hep-ph↗

arXiv2010

Charmed mesons in nuclear matter

We obtain the properties of charmed mesons in dense matter using a coupled-channel approach which accounts for Pauli blocking effects and meson self-energies in a self-consistent manner. We study the behaviour of dynamically-generated baryonic resonances together with the open-charm meson spectral functions in this dense nuclear environment. We discuss the implications of the in-medium properties of open-charm mesons on the $D_{s0}(2317)$ and the predicted X(3700) scalar resonances, and on the formation of $D$-mesic nuclei.

nucl-th↗

arXiv2009

Deeply Bound Kaonic Clusters

In this talk I make a review on the theoretical and experimental situation around the deeply bound kaon clusters, the possible bound kaonic states of nuclear, rather than atomic nature. At the same time I discuss novel developments around other kind of bound kaon clusters, which include states of two mesons and one baryon, with either one or two kaons, and states of a vector meson and two kaons, which explain naturally the observed properties of the X(2175) and Y(4260) resonances.

nucl-th↗

arXiv2009

Charmed hadrons in nuclear medium

We study the properties of charmed hadrons in dense matter within a coupled-channel approach which accounts for Pauli blocking effects and meson self-energies in a self-consistent manner. We analyze the behaviour in this dense environment of dynamically-generated baryonic resonances as well as the open-charm meson spectral functions. We discuss the implications of the in-medium properties of open-charm mesons on the $D_{s0}(2317)$ and the predicted X(3700) scalar resonances.

nucl-th↗

arXiv2009

Couplings in coupled channels versus wave functions: application to the X(3872) resonance

We perform an analytical study of the scattering matrix and bound states in problems with many physical coupled channels. We establish the relationship of the couplings of the states to the different channels, obtained from the residues of the scattering matrix at the poles, with the wave functions for the different channels. The couplings basically reflect the value of the wave functions around the origin in coordinate space. In the concrete case of the X(3872) resonance, understood as a bound state of $\ddn$ and $\ddc$ (and $c.c.$), with the $\ddn$ loosely bound, we find that the couplings to the two channels are essentially equal leading to a state of good isospin I=0 character. This is in spite of having a probability for finding the $\ddn$ state much larger than for $\ddc$ since the loosely bound channel extends further in space. The analytical results, obtained with exact solutions of the Schr\"odinger equation for the wave functions, can be useful in general to interpret results found numerically in the study of problems with unitary coupled channels methods.

hep-ph↗